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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCAACGAAATGGCGTACCAATTGGACAGCAGgtatagttgtttcctcttgccacattcaattttagtttcttatcaatgctacaagattagcaagtgtggctaagacgagaatctcttaccatgcattatttcgtgcag

Basic information

species Oryza sativa
transcript LOC_Os03g49610.1
intron # 9
splice site 5'
intron type U2

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|27554361|gb|CA998261.1|CA998261
EST:     TTCAACGAAATGGCGTACCAATTGGACAGCAG                         GCAAACTCTAATTGGCTTTATATCGTTCCGACTGGCATGTATGGAGCTGTG
genomic: TTCAACGAAATGGCGTACCAATTGGACAGCAGgtatagttgt ... tttcgtgcagGCAAACTCTAATTGGCTTTATATCGTTCCGACTGGCATGTATGGAGCTGTG
EST: gi|58669788|gb|CK058474.1|CK058474
EST:     TTCAACGAAATGGCGTACCAATTGGACAGCAG                         GCAAACTCTAATTGGCTTTATATCGTTCCGACTGGCATGTATGGAGCTGTG
genomic: TTCAACGAAATGGCGTACCAATTGGACAGCAGgtatagttgt ... tttcgtgcagGCAAACTCTAATTGGCTTTATATCGTTCCGACTGGCATGTATGGAGCTGTG
EST: gi|58596985|gb|CK007513.1|CK007513
EST:     TTCAACGAAATGGCGTACCAATTGGACAGCAG                         GCAAACTCTAATTGGCTTTATATCGTTCCGACTGGCATGTATGGAGCTGTG
genomic: TTCAACGAAATGGCGTACCAATTGGACAGCAGgtatagttgt ... tttcgtgcagGCAAACTCTAATTGGCTTTATATCGTTCCGACTGGCATGTATGGAGCTGTG
EST: gi|58673908|gb|CK062594.1|CK062594
EST:     TTCAACGAAATGGCGTACCAATTGGACAGCAG                         GCAAACTCTAATTGGCTTTATATCGTTCCGACTGGCATGTATGGAGCTGTG
genomic: TTCAACGAAATGGCGTACCAATTGGACAGCAGgtatagttgt ... tttcgtgcagGCAAACTCTAATTGGCTTTATATCGTTCCGACTGGCATGTATGGAGCTGTG
EST: gi|58660033|gb|CK048713.1|CK048713
EST:     TTCAACGAAATGGCGTACCAATTGGACAGCAG                         GCAAACTCTAATTGGCTTTATATCGTTCCGACTGGCATGTATGGAGCTGTG
genomic: TTCAACGAAATGGCGTACCAATTGGACAGCAGgtatagttgt ... tttcgtgcagGCAAACTCTAATTGGCTTTATATCGTTCCGACTGGCATGTATGGAGCTGTG
EST: gi|163925553|gb|EG715398.1|EG715398
EST:     TTCAACGAAATGGCGTACCAATTGGACAGCAG                         GCAAACTCTAATTGGCTTTATATCGTTCCGACTGGCATGTATGGAGCTGTG
genomic: TTCAACGAAATGGCGTACCAATTGGACAGCAGgtatagttgt ... tttcgtgcagGCAAACTCTAATTGGCTTTATATCGTTCCGACTGGCATGTATGGAGCTGTG
EST: gi|58674306|gb|CK062992.1|CK062992
EST:     TTCAACGAAATGGCGTACCAATTGGACAGCAG                         GCAAACTCTAATTGGCTTTATATCGTTCCGACTGGCATGTATGGAGCTGTG
genomic: TTCAACGAAATGGCGTACCAATTGGACAGCAGgtatagttgt ... tttcgtgcagGCAAACTCTAATTGGCTTTATATCGTTCCGACTGGCATGTATGGAGCTGTG
EST: gi|58674546|gb|CK063233.1|CK063233
EST:     TTCAACGAAATGGCGTACCAATTGGACAGCAG                         GCAAACTCTAATTGGCTTTATATCGTTCCGACTGGCATGTATGGAGCTGTG
genomic: TTCAACGAAATGGCGTACCAATTGGACAGCAGgtatagttgt ... tttcgtgcagGCAAACTCTAATTGGCTTTATATCGTTCCGACTGGCATGTATGGAGCTGTG
EST: gi|58604470|gb|CK014998.1|CK014998
EST:     TTCAACGAAATGGCGTACCAATTGGACAGCAG                         GCAAACTCTAATTGGCTTTATATCGTTCCGACTGGCATGTATGGAGCTGTG
genomic: TTCAACGAAATGGCGTACCAATTGGACAGCAGgtatagttgt ... tttcgtgcagGCAAACTCTAATTGGCTTTATATCGTTCCGACTGGCATGTATGGAGCTGTG
EST: gi|58597512|gb|CK008040.1|CK008040
EST:     TTCAACGAAATGGCGTACCAATTGGACAGCAG                         GCAAACTCTAATTGGCTTTATATCGTTCCGACTGGCATGTATGGAGCTGTG
genomic: TTCAACGAAATGGCGTACCAATTGGACAGCAGgtatagttgt ... tttcgtgcagGCAAACTCTAATTGGCTTTATATCGTTCCGACTGGCATGTATGGAGCTGTG
EST: gi|58598545|gb|CK009073.1|CK009073
EST:     TTCAACGAAATGGCGTACCAATTGGACAGCAG                         GCAAACTCTAATTGGCTTTATATCGTTCCGACTGGCATGTATGGAGCTGTG
genomic: TTCAACGAAATGGCGTACCAATTGGACAGCAGgtatagttgt ... tttcgtgcagGCAAACTCTAATTGGCTTTATATCGTTCCGACTGGCATGTATGGAGCTGTG
EST: gi|58668081|gb|CK056767.1|CK056767
EST:     TTCAACGAAATGGCGTACCAATTGGACAGCAG                         GCAAACTCTAATTGGCTTTATATCGTTCCGACTGGCATGTATGGAGCTGTG
genomic: TTCAACGAAATGGCGTACCAATTGGACAGCAGgtatagttgt ... tttcgtgcagGCAAACTCTAATTGGCTTTATATCGTTCCGACTGGCATGTATGGAGCTGTG
EST: gi|33684008|gb|CF312247.1|CF312247
EST:     TTCAACGAAATGGCGTACCAATTGGACAGCAG                         GCAAACTCTAATTGGCTTTATATCGTTCCGACTGGCATGTATGGAGCTGTG
genomic: TTCAACGAAATGGCGTACCAATTGGACAGCAGgtatagttgt ... tttcgtgcagGCAAACTCTAATTGGCTTTATATCGTTCCGACTGGCATGTATGGAGCTGTG
EST: gi|27554359|gb|CA998259.1|CA998259
EST:     TTCAACGAAATGGCGTACCAATTGGACAGCAG                         GCAAACTCTAATTGGCTTTATATCGTTCCGACTGGCATGTATGGAGCTGTG
genomic: TTCAACGAAATGGCGTACCAATTGGACAGCAGgtatagttgt ... tttcgtgcagGCAAACTCTAATTGGCTTTATATCGTTCCGACTGGCATGTATGGAGCTGTG
EST: gi|58671037|gb|CK059723.1|CK059723
EST:     TTCAACGAAATGGCGTACCAATTGGACAGCAG                         GCAAACTCTAATTGGCTTTATATCGTTCCGACTGGCATGTATGGAGCTGTG
genomic: TTCAACGAAATGGCGTACCAATTGGACAGCAGgtatagttgt ... tttcgtgcagGCAAACTCTAATTGGCTTTATATCGTTCCGACTGGCATGTATGGAGCTGTG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 75 (upstream exon), 50 (downstream exon)
Score: 28

TTCAACGAAATGGCGTACCAATTGGACAGCAGgtatagttgt ... tttcgtgcagGCAAACTCTAATTGGCTTTATATCGTTCCGACTGGCATGTATGGAGCTGTGAACTACATAAAGGAGAAGTATAATAATCCAACAATCATCATATCTGAAA




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